Topbox for me everytime
Not cool or gonna add cred but waterproof an more importantly, secure. I've had one - the same actually - on my last 4 bikes. That's a Thundrcat, BMW R1100 rs, z750 s and KTM 950sm. That's a total of 250,000 miles, not bad for 60 quid!!!

A top box is secure, convenient and makes like Givi will be very well made and waterproof. They are not cheap but the advantage is that is can be transferered to your next bike with just the addition of a fitting kit for your mew machine. The disadvantage is that is puts weight up high and beyond the back wheel.

Saddle bags, as in the soft variety put the weight lower down but are not secure. You'll need to make some provision to ensure that they do not scratch your paintwork and you will need to ensure that are securely attached to your bike so that they do not move when you are riding.

For light loads over short journeys many find a rucksack ideal for the job. Of course, that can't be left on the bike when you park up.

Saddlebags
I hate topboxes cus' they make you look like you're delivering pizzas or body parts!

They are probably more practical but not necessarily more waterproof. Most saddlebags come with rain covers but some Kreiger bags are completely waterproof anyway. I've just bought some Cameron Barker panniers and they are completely waterproof, semi-hard rolltop closure and they work great. I've been riding with them for two weeks and even gave them a hose test, they are also HUGE! Can fit a lot more in them than you expect. Top boxes are not always waterproof, a couple of mates have top boxes and both of them leak when the weather turns really nasty.

Saddlebags are not as secure as topboxes but look nicer on a sportier bike so it depends on what you'll be using them for and how often?